Interleaved echo-planar imaging (EPI) is susceptible to significant ghosting artifacts, resulting primarily from system time delays that cause data matrix misregistration. Most EPI applications rely on "reference scans" to measure delays, and post-processing algorithms are used to correct these errors. Unfortunately, delay estimates made with most reference scan techniques are object dependent, since they are biased by magnetic field inhomogeneities and chemical shift. The current work describes the effects of field inhomogeneities and their influence on system time delay estimation. Subsequently, a new, object-independent "balanced" reference method using two readout echo trains is proposed for time delay measurements.